Query         537021.9.peg.473_1
Match_columns 165
No_of_seqs    132 out of 531
Neff          4.7 
Searched_HMMs 39220
Date          Wed May 25 02:08:42 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_473.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK09111 DNA polymerase III su 100.0 3.1E-37   8E-42  239.1  15.1  109   56-164   455-578 (600)
  2 pfam12362 DUF3646 DNA polymera 100.0 7.1E-37 1.8E-41  237.1  12.5  101   60-160     2-117 (117)
  3 PRK06645 DNA polymerase III su 100.0 1.4E-28 3.6E-33  188.4  13.7   99   63-162   400-506 (507)
  4 PRK06674 DNA polymerase III su  98.4 3.4E-06 8.6E-11   57.2   9.8   98   62-161   440-563 (563)
  5 PRK08770 DNA polymerase III su  97.8 0.00024 6.2E-09   46.3   9.5   99   65-164   539-663 (663)
  6 PRK05563 DNA polymerase III su  97.6  0.0012 3.1E-08   42.2  10.5   95   62-160   437-539 (541)
  7 PRK05648 DNA polymerase III su  97.3   0.013 3.3E-07   36.1  12.1   98   66-164   577-700 (705)
  8 PRK12323 DNA polymerase III su  96.2    0.11 2.9E-06   30.6  10.4   97   65-162   600-719 (721)
  9 PRK06872 DNA polymerase III su  96.1   0.085 2.2E-06   31.4   9.3   94   68-162   576-696 (696)
 10 PRK08691 DNA polymerase III su  95.1    0.16   4E-06   29.8   7.6   86   78-164   587-702 (704)
 11 PRK07994 DNA polymerase III su  93.7    0.63 1.6E-05   26.3   8.9   92   69-162   525-643 (643)
 12 PRK07003 DNA polymerase III su  90.0     1.7 4.3E-05   23.7  11.2   97   66-163   685-804 (816)
 13 PRK08853 DNA polymerase III su  80.5     5.2 0.00013   20.9   9.3   93   68-162   600-717 (717)
 14 PRK08451 DNA polymerase III su  74.0       8  0.0002   19.8   8.3   96   61-157   375-521 (523)
 15 PTZ00105 60S ribosomal protein  57.1      11 0.00028   19.0   2.9   52   63-114   105-156 (164)
 16 pfam10273 WGG Pre-rRNA-process  49.2       3 7.7E-05   22.3  -1.0   50  109-158     2-51  (82)
 17 pfam01610 Transposase_12 Trans  48.6      24 0.00061   17.0   3.8   63   88-160    18-82  (100)
 18 pfam05637 Glyco_transf_34 gala  44.4      15 0.00039   18.1   2.0   18  139-156    62-79  (242)
 19 COG0193 Pth Peptidyl-tRNA hydr  39.5      32 0.00082   16.2   3.0   61   90-155    95-156 (190)
 20 KOG1559 consensus               38.9      25 0.00065   16.8   2.4   68   63-130   156-224 (340)
 21 PRK06156 hypothetical protein;  38.2      35 0.00089   16.0   5.8   69   83-151   375-451 (522)
 22 pfam10411 DsbC_N Disulfide bon  36.7      27  0.0007   16.6   2.3   19  145-163     3-21  (54)
 23 PRK10553 assembly protein for   32.8      33 0.00083   16.2   2.1   16  142-157    20-35  (87)
 24 TIGR01734 D-ala-DACP-lig D-ala  32.7      26 0.00066   16.8   1.6   19  140-158   278-296 (513)
 25 pfam04461 DUF520 Protein of un  30.9      46  0.0012   15.3   5.4   82   72-154    57-148 (160)
 26 KOG2492 consensus               29.2      49  0.0013   15.2   4.4   69   89-157   318-397 (552)
 27 pfam11396 DUF2874 Protein of u  28.5      51  0.0013   15.1   3.0   22  142-163     4-25  (54)
 28 TIGR01091 upp uracil phosphori  24.4      61  0.0015   14.6   2.8   20  140-159    83-102 (213)
 29 PRK05758 F0F1 ATP synthase sub  23.6      63  0.0016   14.5   3.8   85   44-130    54-140 (175)
 30 pfam03927 NapD NapD protein. U  22.2      63  0.0016   14.5   2.1   17  142-158    17-33  (78)
 31 PRK05412 nucleotide-binding pr  21.6      69  0.0018   14.3   5.4   81   73-154    58-148 (161)
 32 TIGR02258 2_5_ligase 2'-5' RNA  21.4      69  0.0018   14.3   5.0   61   65-131    15-77  (189)
 33 PRK13552 frdB fumarate reducta  21.3      66  0.0017   14.4   2.0   45   87-131    79-127 (240)
 34 cd01791 Ubl5 UBL5 (also known   20.1      74  0.0019   14.1   3.0   23  105-127    19-41  (73)

No 1  
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=100.00  E-value=3.1e-37  Score=239.13  Aligned_cols=109  Identities=29%  Similarity=0.524  Sum_probs=99.4

Q ss_pred             CCCCCCCCHHHHHHHHHHCCHHHHHHHHHHCCCCEEECCCEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCH
Q ss_conf             13471244899999998618266799997264004504980899977899977999999999986099259999689741
Q 537021.9.peg.4   56 SACTPDNYTKQLIELCEKNHDYKMVEMLQRFLHVVSFELGRLEVSFLKEIPEDFIENLATKLKNWTGEDWEIRFSLGRCC  135 (165)
Q Consensus        56 ~~~~~~nsf~~lveL~~~~rei~Lk~~Le~~VrLVsFe~GrIei~~~~~a~~~l~~~Ls~~L~~wTG~rW~VslS~g~~~  135 (165)
                      .....+++|+||++||+++||+.|+|+||+|||||||++|+|+|++++++|++|+++|+.+|.+|||+||+|++|.+.+.
T Consensus       455 ~~~~~i~SF~dLI~L~~~kkEi~Lk~eLE~nVrLVsFe~GrIeIsfnE~l~knfik~Ls~kL~eWTG~RWiIslSke~G~  534 (600)
T PRK09111        455 PPAVPINSFEDIVALAREKRDIKLKALVENDVRLVRFEPGRLEFRLTEDAPRDLANRLARKLEEWTGRRWTVSVSNEGGQ  534 (600)
T ss_pred             CCCCCCCCHHHHHHHHHHCCHHHHHHHHHHCEEEEEECCCEEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCC
T ss_conf             54467668999999998613088999999670788844883788657888776999999999998689749996678887


Q ss_pred             ---------------HHHHCCHHHHHHHHHCCCCEEEEEEECCC
Q ss_conf             ---------------36653969999998679977898774588
Q 537021.9.peg.4  136 ---------------EYFEIDSDIKAVRTIFPTAQVVCIRTIPN  164 (165)
Q Consensus       136 ---------------e~~~~dp~V~avl~~FPgAeI~~VR~~p~  164 (165)
                                     +.++.||+|++||++||||+|++||.++.
T Consensus       535 ~Tl~Ekk~~~k~e~~e~ak~~P~VKkILe~FPdAEIidVr~l~~  578 (600)
T PRK09111        535 PTLAEQEAAAREEREAAAEADPLVQAVLAAFPGAKIVDVRDLAP  578 (600)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCEEEEEECCCC
T ss_conf             79999999999999999875979999998689997887112786


No 2  
>pfam12362 DUF3646 DNA polymerase III gamma and tau subunits C terminal. This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with pfam00004. The proteins in this family are frequently annotated as the gamma and tau subunits of DNA polymerase III, however there is little accompanying literature to back this up.
Probab=100.00  E-value=7.1e-37  Score=237.06  Aligned_cols=101  Identities=29%  Similarity=0.458  Sum_probs=94.2

Q ss_pred             CCCCHHHHHHHHHHCCHHHHHHHHHHCCCCEEECCCEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCH----
Q ss_conf             1244899999998618266799997264004504980899977899977999999999986099259999689741----
Q 537021.9.peg.4   60 PDNYTKQLIELCEKNHDYKMVEMLQRFLHVVSFELGRLEVSFLKEIPEDFIENLATKLKNWTGEDWEIRFSLGRCC----  135 (165)
Q Consensus        60 ~~nsf~~lveL~~~~rei~Lk~~Le~~VrLVsFe~GrIei~~~~~a~~~l~~~Ls~~L~~wTG~rW~VslS~g~~~----  135 (165)
                      .++||+|||+||+++||+.|+++|++|||||||+||+|+|++++++|++|+++|+++|.+|||+||+|++|.+.+.    
T Consensus         2 ~i~sf~dlv~l~~~~re~~L~~~l~~~VrlVsf~~G~Iei~~~~~~~~~l~~~L~~~L~~wTg~rW~Vs~s~~~g~~Tl~   81 (117)
T pfam12362         2 RIASFEDLVALARAKRDIKLKVEVERDVRLVSFEPGRIEFRPTPGAPRDLAQRLGRKLQEWTGRRWAVSLSNEGGAPTLA   81 (117)
T ss_pred             CCCCHHHHHHHHHHCCHHHHHHHHHHCCEEEEEECCEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHH
T ss_conf             75899999999997675989999997837898408978997589998779999999999973998099965789987899


Q ss_pred             -----------HHHHCCHHHHHHHHHCCCCEEEEEE
Q ss_conf             -----------3665396999999867997789877
Q 537021.9.peg.4  136 -----------EYFEIDSDIKAVRTIFPTAQVVCIR  160 (165)
Q Consensus       136 -----------e~~~~dp~V~avl~~FPgAeI~~VR  160 (165)
                                 +.+++||+|++||.+||||+|++||
T Consensus        82 E~~~~~~~~~~~~~~~~P~v~avl~~FP~A~I~~Vr  117 (117)
T pfam12362        82 EQEAAAKEALRADARAHPLVQAVLAAFPGAKIVDVR  117 (117)
T ss_pred             HHHHHHHHHHHHHHHCCHHHHHHHHHCCCCEEEECC
T ss_conf             999999999999998798999999879898877229


No 3  
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=99.96  E-value=1.4e-28  Score=188.36  Aligned_cols=99  Identities=18%  Similarity=0.270  Sum_probs=91.4

Q ss_pred             CHHHHHHHHHHCCHHHHHHHHHHCCCCEEECCCEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCH-------
Q ss_conf             4899999998618266799997264004504980899977899977999999999986099259999689741-------
Q 537021.9.peg.4   63 YTKQLIELCEKNHDYKMVEMLQRFLHVVSFELGRLEVSFLKEIPEDFIENLATKLKNWTGEDWEIRFSLGRCC-------  135 (165)
Q Consensus        63 sf~~lveL~~~~rei~Lk~~Le~~VrLVsFe~GrIei~~~~~a~~~l~~~Ls~~L~~wTG~rW~VslS~g~~~-------  135 (165)
                      .+.|++++|.++||++|+|+||+||+||||++|+||| ++++++++|+++|+.+|.+|||+||+|++|...+.       
T Consensus       400 ei~d~i~l~~~~kEi~Lky~LenNV~LVsF~~g~IeI-~~~~l~~nfik~Ls~kL~~WTg~RWiItlske~g~~t~K~~l  478 (507)
T PRK06645        400 EIVDFLKYLYKNNEIDIYYFLLNHTELKNLSDNRLEF-VSLEVTSKIKKQIEDLLAAFTNEKWEIIIIKEQNKQTLKNQL  478 (507)
T ss_pred             CHHHHHHHHHHCCHHHHHHHHHHCCEEEEEECCEEEE-ECCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHH
T ss_conf             3999999998766076799999672479820886788-567676889999999999985787699985476836599999


Q ss_pred             -HHHHCCHHHHHHHHHCCCCEEEEEEEC
Q ss_conf             -366539699999986799778987745
Q 537021.9.peg.4  136 -EYFEIDSDIKAVRTIFPTAQVVCIRTI  162 (165)
Q Consensus       136 -e~~~~dp~V~avl~~FPgAeI~~VR~~  162 (165)
                       +.++..+.+++|+..||+|||+||+..
T Consensus       479 i~~~k~s~~~k~vl~~FPdAeLiDI~~k  506 (507)
T PRK06645        479 IQKIEASNDFGLIKKHFPNVKISDILLK  506 (507)
T ss_pred             HHHHHCCHHHHHHHHHCCCCEEEEEECC
T ss_conf             9998739999999985979858884268


No 4  
>PRK06674 DNA polymerase III subunits gamma and tau; Validated
Probab=98.41  E-value=3.4e-06  Score=57.16  Aligned_cols=98  Identities=12%  Similarity=0.054  Sum_probs=75.0

Q ss_pred             CCHHHHHHHHHHCCHHHHHHHHHHCCCCEEECCCEEEEEECCCC-------CHH-HHHHHHHHHHHHCCCCEEEEEECCC
Q ss_conf             44899999998618266799997264004504980899977899-------977-9999999999860992599996897
Q 537021.9.peg.4   62 NYTKQLIELCEKNHDYKMVEMLQRFLHVVSFELGRLEVSFLKEI-------PED-FIENLATKLKNWTGEDWEIRFSLGR  133 (165)
Q Consensus        62 nsf~~lveL~~~~rei~Lk~~Le~~VrLVsFe~GrIei~~~~~a-------~~~-l~~~Ls~~L~~wTG~rW~VslS~g~  133 (165)
                      +...++++.+.+++.+.+.+ |-...++|...++.+.+.|....       +.+ +...+...|.+|||.+|.|......
T Consensus       440 ~~W~~il~~lk~~~~~~~~a-ll~~~~Pvaa~~~~~vl~F~~~~~~~~~~~~~~~~~~~l~~~l~~~~g~~~~iv~v~~~  518 (563)
T PRK06674        440 AVWGELLGRLKQQNKVSHAA-LLENSEPVAASDDAFVLAFKYEIHCKMASENREAVDTNVEQILFELLSKRLNMIAIPKS  518 (563)
T ss_pred             HHHHHHHHHHHHCCHHHHHH-HHCCCCEEEECCCCEEEEECCHHHHHHHCCCHHHHHHHHHHHHHHHHCCCEEEEEEEHH
T ss_conf             89999999998415687999-98079125435992799958488999862557889999999999995897279995278


Q ss_pred             CH------------------HHHHCCHHHHHHHHHCCCCEEEEEEE
Q ss_conf             41------------------36653969999998679977898774
Q 537021.9.peg.4  134 CC------------------EYFEIDSDIKAVRTIFPTAQVVCIRT  161 (165)
Q Consensus       134 ~~------------------e~~~~dp~V~avl~~FPgAeI~~VR~  161 (165)
                      .+                  +..+.||+|++++..| |+++|.|+.
T Consensus       519 ~w~~iR~e~i~~~~~~~~~~~~~~edp~V~eA~~lF-G~dlVeIkd  563 (563)
T PRK06674        519 EWGKIREDFLQREGGSSEESPEKEEDPLIEEAKKLV-GQELIEIKE  563 (563)
T ss_pred             HHHHHHHHHHHHCCCCHHHCCCCCCCHHHHHHHHHC-CCCEEEECC
T ss_conf             789999999985255510125543586999999863-986157349


No 5  
>PRK08770 DNA polymerase III subunits gamma and tau; Validated
Probab=97.82  E-value=0.00024  Score=46.29  Aligned_cols=99  Identities=22%  Similarity=0.186  Sum_probs=77.0

Q ss_pred             HHHHHHHHHCCHHHHHHHHHHCCCCEEECCCEEEEEECCC----CCHHHHHHHHHHHHHHCCCCEEEEEECCCCH-----
Q ss_conf             9999999861826679999726400450498089997789----9977999999999986099259999689741-----
Q 537021.9.peg.4   65 KQLIELCEKNHDYKMVEMLQRFLHVVSFELGRLEVSFLKE----IPEDFIENLATKLKNWTGEDWEIRFSLGRCC-----  135 (165)
Q Consensus        65 ~~lveL~~~~rei~Lk~~Le~~VrLVsFe~GrIei~~~~~----a~~~l~~~Ls~~L~~wTG~rW~VslS~g~~~-----  135 (165)
                      .+-.+++..-.=-.+..+|=-|--|+++..|.+.+.+.+.    ....-..+|...|.++-|+.+.|.+..|...     
T Consensus       539 ~~W~~lV~qL~L~GlarqLAlNs~Lvs~~d~~L~L~L~~~~~hL~ne~~~erL~qALse~lG~~V~L~Ievg~~~~eTPa  618 (663)
T PRK08770        539 EQWLELVTRSGLNGPSRQLAANAAFIGHRDGVLRLALAPGFEYLNSERSIANLAQALAPVLGNAPRIVIETGSADVETLH  618 (663)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHEEECCEEEEEECHHHHHHCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCHH
T ss_conf             26999998669817999999834454236898999978887875699999999999999978997999987998886999


Q ss_pred             ---------------HHHHCCHHHHHHHHHCCCCEEE--EEEECCC
Q ss_conf             ---------------3665396999999867997789--8774588
Q 537021.9.peg.4  136 ---------------EYFEIDSDIKAVRTIFPTAQVV--CIRTIPN  164 (165)
Q Consensus       136 ---------------e~~~~dp~V~avl~~FPgAeI~--~VR~~p~  164 (165)
                                     +.+++||.|+..++.| ||+|+  |||++++
T Consensus       619 ~r~~r~~aErqqqAeqaLqnDP~VQ~L~q~F-gAqL~~eSIrP~D~  663 (663)
T PRK08770        619 ERANRQKGERQSAAETAFMNDPTVQLLIQQQ-GARVVPDSIRPYDE  663 (663)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH-CCEECCCCCCCCCC
T ss_conf             9999999999999999996298999999972-99987787688999


No 6  
>PRK05563 DNA polymerase III subunits gamma and tau; Validated
Probab=97.61  E-value=0.0012  Score=42.19  Aligned_cols=95  Identities=13%  Similarity=0.174  Sum_probs=71.7

Q ss_pred             CCHHHHHHHHHHCCHHHHHHHHHHCCCCEEECCCEEEEEECCCCC--------HHHHHHHHHHHHHHCCCCEEEEEECCC
Q ss_conf             448999999986182667999972640045049808999778999--------779999999999860992599996897
Q 537021.9.peg.4   62 NYTKQLIELCEKNHDYKMVEMLQRFLHVVSFELGRLEVSFLKEIP--------EDFIENLATKLKNWTGEDWEIRFSLGR  133 (165)
Q Consensus        62 nsf~~lveL~~~~rei~Lk~~Le~~VrLVsFe~GrIei~~~~~a~--------~~l~~~Ls~~L~~wTG~rW~VslS~g~  133 (165)
                      .++.++++.+.++|.+.+++.| .+.++|+|+.|.|.+.+.+.-.        .....-+...+.+-+|++|.|.+....
T Consensus       437 ~~W~~ILe~lk~~r~~~l~alL-~~~~pv~~~~~~l~I~f~~~~~f~~~~l~~~e~~~~ie~i~~e~~g~~~~i~~v~~~  515 (541)
T PRK05563        437 KVWKDILEAFKARRKMVLYAAL-VTGKLVKCKKGVITINYKKEYAFNKKRLEKPENKKVVEEIFSEVLKEKVRVKYVVEE  515 (541)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHH-HCCEEEEEECCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEC
T ss_conf             8999999998852542099998-559579987998999989831778998612778999999999996998169999845


Q ss_pred             CHHHHHCCHHHHHHHHHCCCCEEEEEE
Q ss_conf             413665396999999867997789877
Q 537021.9.peg.4  134 CCEYFEIDSDIKAVRTIFPTAQVVCIR  160 (165)
Q Consensus       134 ~~e~~~~dp~V~avl~~FPgAeI~~VR  160 (165)
                      ... .+.+| .+.+.+.| |++++.|.
T Consensus       516 ~~~-~e~~~-~~~~k~~f-g~~~~ei~  539 (541)
T PRK05563        516 EIK-EEKDP-EEILKNTF-GEEILEII  539 (541)
T ss_pred             CCC-CCCCH-HHHHHHHC-CCCCEEEC
T ss_conf             654-44689-99999865-86435634


No 7  
>PRK05648 DNA polymerase III subunits gamma and tau; Reviewed
Probab=97.26  E-value=0.013  Score=36.15  Aligned_cols=98  Identities=13%  Similarity=0.107  Sum_probs=77.9

Q ss_pred             HHHHHHHHCCHHHHHHHHHHCCCCEEECCCEEEEEECCC----CCHHHHHHHHHHHHHHCCCCEEEEEECCCC-------
Q ss_conf             999999861826679999726400450498089997789----997799999999998609925999968974-------
Q 537021.9.peg.4   66 QLIELCEKNHDYKMVEMLQRFLHVVSFELGRLEVSFLKE----IPEDFIENLATKLKNWTGEDWEIRFSLGRC-------  134 (165)
Q Consensus        66 ~lveL~~~~rei~Lk~~Le~~VrLVsFe~GrIei~~~~~----a~~~l~~~Ls~~L~~wTG~rW~VslS~g~~-------  134 (165)
                      +-..++..-.=-.|..+|=-|--|++++.+.+.+.+.+.    ....-..+|...|.++-|+.=.|.+..|..       
T Consensus       577 ~Wa~lV~qL~L~GLvrQLAlNS~L~~~~gd~l~L~L~~~q~hL~ne~~~erL~eALSe~lG~~V~L~Ievge~~~eTPae  656 (705)
T PRK05648        577 EWLELFPQLGVSGMTGSIAANCTLIAADGDHWLLHLDPGQSALFNATQQRRLNDALNQYLGRTLKLEIELIKPEQETPAQ  656 (705)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCEEEEEECCEEEEEECHHHHHHCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCHHH
T ss_conf             39999987698089999996203013789999999888978657999999999999998689979999879977779999


Q ss_pred             -------------HHHHHCCHHHHHHHHHCCCCEEE--EEEECCC
Q ss_conf             -------------13665396999999867997789--8774588
Q 537021.9.peg.4  135 -------------CEYFEIDSDIKAVRTIFPTAQVV--CIRTIPN  164 (165)
Q Consensus       135 -------------~e~~~~dp~V~avl~~FPgAeI~--~VR~~p~  164 (165)
                                   .+.+++||.|+.+++.| ||+|+  |||++.+
T Consensus       657 ~r~ri~qErqqqAeqaL~nDP~VQ~L~q~F-gAeLde~SIrPID~  700 (705)
T PRK05648        657 AAARRRAERQRAAEASIHADPLIQQMIQQF-GAVVREDTIEPVEA  700 (705)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHC-CCEECCCCEEECCC
T ss_conf             999999999999999997098999999981-99986786205766


No 8  
>PRK12323 DNA polymerase III subunits gamma and tau; Provisional
Probab=96.18  E-value=0.11  Score=30.63  Aligned_cols=97  Identities=18%  Similarity=0.150  Sum_probs=73.7

Q ss_pred             HHHHHHHHHCCHHHHHHHHHHCCCCEEECCCEEEEEECCC--CCHHHHHHHHHHHHHHCCCCEEEEEECCCC--------
Q ss_conf             9999999861826679999726400450498089997789--997799999999998609925999968974--------
Q 537021.9.peg.4   65 KQLIELCEKNHDYKMVEMLQRFLHVVSFELGRLEVSFLKE--IPEDFIENLATKLKNWTGEDWEIRFSLGRC--------  134 (165)
Q Consensus        65 ~~lveL~~~~rei~Lk~~Le~~VrLVsFe~GrIei~~~~~--a~~~l~~~Ls~~L~~wTG~rW~VslS~g~~--------  134 (165)
                      .+-..++..-.=..|..+|-.+--|++++.+.+.++....  .......+|...|.+.-|+.-.+.+..|..        
T Consensus       600 ~~W~~lv~~L~l~gl~~qLA~ns~l~~~~~~~l~Lr~~~~~L~~~~~~~~L~~ALs~~~G~~v~l~Ie~g~~~~Tpa~~~  679 (721)
T PRK12323        600 GDWPELAARLPLTGLAQQLARQSELAGVVGDTVHLRVPVAALAESEVRERLQTVLCEHFGQPVRVECEVGAVDGTAAAVD  679 (721)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCEEEEECCHHHHCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCHHHHH
T ss_conf             55999998669806999999711554135998898077467589999999999999986898689998699888989999


Q ss_pred             -----------HHHHHCCHHHHHHHHHCCCCEEE--EEEEC
Q ss_conf             -----------13665396999999867997789--87745
Q 537021.9.peg.4  135 -----------CEYFEIDSDIKAVRTIFPTAQVV--CIRTI  162 (165)
Q Consensus       135 -----------~e~~~~dp~V~avl~~FPgAeI~--~VR~~  162 (165)
                                 .+.++.||.|+.++..| ||+|+  +||+.
T Consensus       680 ~~~~~er~~~A~~aL~~Dp~Vq~L~~~F-gAel~~~SIrP~  719 (721)
T PRK12323        680 AIERAERQRAAEDAIAADPFVQALVRDF-GGQVVPGSIQPP  719 (721)
T ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHH-CCEECCCCCCCC
T ss_conf             9999999999999996099999999982-999855865889


No 9  
>PRK06872 DNA polymerase III subunits gamma and tau; Provisional
Probab=96.09  E-value=0.085  Score=31.35  Aligned_cols=94  Identities=18%  Similarity=0.220  Sum_probs=70.1

Q ss_pred             HHHHHHCCHHHHHHHHHHCCCCEEECCCEEEEEECCC----CCHHHHHHHHHHHHHHCCCCEEEEEECCCC---------
Q ss_conf             9999861826679999726400450498089997789----997799999999998609925999968974---------
Q 537021.9.peg.4   68 IELCEKNHDYKMVEMLQRFLHVVSFELGRLEVSFLKE----IPEDFIENLATKLKNWTGEDWEIRFSLGRC---------  134 (165)
Q Consensus        68 veL~~~~rei~Lk~~Le~~VrLVsFe~GrIei~~~~~----a~~~l~~~Ls~~L~~wTG~rW~VslS~g~~---------  134 (165)
                      ..++..-.=..|..+|=-|--+++...+.+.+.+.+.    ....-..+|...|.++-|+...+.+.-|..         
T Consensus       576 ~~li~qL~L~GlvrQLA~NSvl~~~~gd~l~L~L~~~q~hL~nd~~~erL~~ALse~lG~~V~L~IevGd~~~~eTPae~  655 (696)
T PRK06872        576 TKIVERLGLTGLSKQLALNSVLLSKTGDEIKLGLRSAKSHLDNDRSIKSLAQALSKLQGKDIRLTISLGDDANLKTPLEY  655 (696)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHHHEECCCEEEEEECHHHHHHCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCHHHH
T ss_conf             99998769827999999843111122998899877898876699999999999999878995899998998777799999


Q ss_pred             ------------HHHHHCCHHHHHHHHHCCCCEE--EEEEEC
Q ss_conf             ------------1366539699999986799778--987745
Q 537021.9.peg.4  135 ------------CEYFEIDSDIKAVRTIFPTAQV--VCIRTI  162 (165)
Q Consensus       135 ------------~e~~~~dp~V~avl~~FPgAeI--~~VR~~  162 (165)
                                  .+.++.||.|+..++.| ||+|  -+||++
T Consensus       656 r~ri~qEr~~qA~~sL~~DP~VQ~L~q~F-gAqLde~SIrPl  696 (696)
T PRK06872        656 RRQIYQALREKAKKALQKDEKLQLLLQEF-DAELDLSSIRPV  696 (696)
T ss_pred             HHHHHHHHHHHHHHHHHCCHHHHHHHHHC-CCEECCCCEEEC
T ss_conf             99999999999999997398999999970-988857871009


No 10 
>PRK08691 DNA polymerase III subunits gamma and tau; Validated
Probab=95.05  E-value=0.16  Score=29.78  Aligned_cols=86  Identities=14%  Similarity=0.145  Sum_probs=61.1

Q ss_pred             HHHHHHHHCCCCEEECC--CEEEEEECCC----CCHHHHHHHHHHHHHHCCCCEEEEEECC-----CC------------
Q ss_conf             67999972640045049--8089997789----9977999999999986099259999689-----74------------
Q 537021.9.peg.4   78 KMVEMLQRFLHVVSFEL--GRLEVSFLKE----IPEDFIENLATKLKNWTGEDWEIRFSLG-----RC------------  134 (165)
Q Consensus        78 ~Lk~~Le~~VrLVsFe~--GrIei~~~~~----a~~~l~~~Ls~~L~~wTG~rW~VslS~g-----~~------------  134 (165)
                      .+..+|-.+--++.|..  |.|.+.+.+.    .+..-..+|...|.+.-|+.+.+.+..|     ..            
T Consensus       587 g~~~~lA~~~~l~~~~~d~~~l~L~l~~~~~hL~~~~~~~~L~~ALs~~~g~~v~l~i~~~~~~~~~~TP~~~~~~~~~e  666 (704)
T PRK08691        587 GAAQMPAQHSAWTEYHPDTGLMVLAMTAEARATADKKRLDKIRDTLAQAYGLQLTLQTQDWRDEAGRETPAMQDKRVQAE  666 (704)
T ss_pred             HHHHHHHHHHHHHHCCCCCCEEEEEECHHHHHHCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCHHHHHHHHHHH
T ss_conf             09999999998876047788699962789775379999999999999986898699999657886553999999999999


Q ss_pred             -----HHHHHCCHHHHHHHHHCCCCEEE--EEEECCC
Q ss_conf             -----13665396999999867997789--8774588
Q 537021.9.peg.4  135 -----CEYFEIDSDIKAVRTIFPTAQVV--CIRTIPN  164 (165)
Q Consensus       135 -----~e~~~~dp~V~avl~~FPgAeI~--~VR~~p~  164 (165)
                           .+.+++||.|+..+..| ||+|+  |||++-|
T Consensus       667 r~~~A~~~l~~Dp~VQ~L~~~F-~A~lde~SIrP~a~  702 (704)
T PRK08691        667 DRQKAQALLEADPAAQKILQAF-GAQWQPESLELAAN  702 (704)
T ss_pred             HHHHHHHHHHHCHHHHHHHHHH-CCEECCCCCCCCCC
T ss_conf             9999999997198999999982-99875670068989


No 11 
>PRK07994 DNA polymerase III subunits gamma and tau; Validated
Probab=93.66  E-value=0.63  Score=26.26  Aligned_cols=92  Identities=18%  Similarity=0.148  Sum_probs=62.9

Q ss_pred             HHHHHCCHHHHHHHHHHCCCCEEECCCEEEEEECCC----CCHHHHHHHHHHHHHHCCCCEEEEEECC----C-------
Q ss_conf             999861826679999726400450498089997789----9977999999999986099259999689----7-------
Q 537021.9.peg.4   69 ELCEKNHDYKMVEMLQRFLHVVSFELGRLEVSFLKE----IPEDFIENLATKLKNWTGEDWEIRFSLG----R-------  133 (165)
Q Consensus        69 eL~~~~rei~Lk~~Le~~VrLVsFe~GrIei~~~~~----a~~~l~~~Ls~~L~~wTG~rW~VslS~g----~-------  133 (165)
                      .++..-+=..|..+|--|- ++....|.+.+.+.+.    .......+|...|.++-|+.=.+++..+    .       
T Consensus       525 ~lv~qL~L~GLvrqLAlns-~~e~~~~~l~L~L~~~q~hL~n~~~~erL~~ALs~~lG~~v~L~I~~~d~~a~~TPae~r  603 (643)
T PRK07994        525 AQVSQLSLPKLVEQVALNA-WKEESDNAVCLHLRSSQRHLNSRGAQQKLAEALSELKGSTVELTIVEDDNPAVRTPLEWR  603 (643)
T ss_pred             HHHHHCCCHHHHHHHHHHH-HHHEECCEEEEEECHHHHHHCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCHHHHH
T ss_conf             9999737418999999988-863149989999767878758999999999999998589879999847870217999999


Q ss_pred             ----------CHHHHHCCHHHHHHHHHCCCCEE--EEEEEC
Q ss_conf             ----------41366539699999986799778--987745
Q 537021.9.peg.4  134 ----------CCEYFEIDSDIKAVRTIFPTAQV--VCIRTI  162 (165)
Q Consensus       134 ----------~~e~~~~dp~V~avl~~FPgAeI--~~VR~~  162 (165)
                                ..+.+++||.|+..++.| ||+|  -|||++
T Consensus       604 ~~i~qEr~~qA~eaL~~DP~VQ~L~q~F-dA~L~e~SIrPI  643 (643)
T PRK07994        604 QAIYEEKLAQARESIIADNNIQTLRRFF-DAELDEESIRPI  643 (643)
T ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHC-CCEECCCCCCCC
T ss_conf             9999999999999997298999999980-988866772129


No 12 
>PRK07003 DNA polymerase III subunits gamma and tau; Validated
Probab=90.00  E-value=1.7  Score=23.73  Aligned_cols=97  Identities=15%  Similarity=0.178  Sum_probs=76.7

Q ss_pred             HHHHHHHHCCHHHHHHHHHHCCCCEEECCCEEEEEECC--CCCHHHHHHHHHHHHHHCCCCEEEEEECCCCH--------
Q ss_conf             99999986182667999972640045049808999778--99977999999999986099259999689741--------
Q 537021.9.peg.4   66 QLIELCEKNHDYKMVEMLQRFLHVVSFELGRLEVSFLK--EIPEDFIENLATKLKNWTGEDWEIRFSLGRCC--------  135 (165)
Q Consensus        66 ~lveL~~~~rei~Lk~~Le~~VrLVsFe~GrIei~~~~--~a~~~l~~~Ls~~L~~wTG~rW~VslS~g~~~--------  135 (165)
                      +-..|+.+-.=..|..+|=-|-.|+.++.+.+.+++..  .++.....+|...|.+.-|+.-.|++.-|...        
T Consensus       685 ~W~~Li~~L~l~Glv~QLAlNS~l~~~~g~~l~L~v~~~q~~~~~~~~~L~~ALs~~lG~~v~l~IevG~~~~Tpa~l~~  764 (816)
T PRK07003        685 EWPTLAARLPLKGVAYQLAFNSELTAVDAGTLKLSVPVPQYADAAQVAKLKAALADALGKPVEVAVEVGPARRTAAALDA  764 (816)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHCEEECCCCCEEEECCCHHHHCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCHHHHHH
T ss_conf             49999986785249999996356631348755653786785078999999999999868975899987998899899999


Q ss_pred             -----------HHHHCCHHHHHHHHHCCCCEEE--EEEECC
Q ss_conf             -----------3665396999999867997789--877458
Q 537021.9.peg.4  136 -----------EYFEIDSDIKAVRTIFPTAQVV--CIRTIP  163 (165)
Q Consensus       136 -----------e~~~~dp~V~avl~~FPgAeI~--~VR~~p  163 (165)
                                 +.+++||.|+..+.-| ||+|+  +||++-
T Consensus       765 ~~ra~rq~qA~~~i~~DP~VQ~L~r~F-gA~i~~dSIrPi~  804 (816)
T PRK07003        765 AARAARQREAEQEIHADPFVQQLVREF-GARIVEGSVRPLA  804 (816)
T ss_pred             HHHHHHHHHHHHHHHHCHHHHHHHHHC-CCEECCCCEEECC
T ss_conf             999999999999986098999999973-9888379444788


No 13 
>PRK08853 DNA polymerase III subunits gamma and tau; Validated
Probab=80.52  E-value=5.2  Score=20.90  Aligned_cols=93  Identities=20%  Similarity=0.270  Sum_probs=62.8

Q ss_pred             HHHHHHCCHHHHHHHHHHCCCCEEECCCEEEEEECCCC----CHHHHHHHHHHHHHHCCCCEEEEEECCCCH--------
Q ss_conf             99998618266799997264004504980899977899----977999999999986099259999689741--------
Q 537021.9.peg.4   68 IELCEKNHDYKMVEMLQRFLHVVSFELGRLEVSFLKEI----PEDFIENLATKLKNWTGEDWEIRFSLGRCC--------  135 (165)
Q Consensus        68 veL~~~~rei~Lk~~Le~~VrLVsFe~GrIei~~~~~a----~~~l~~~Ls~~L~~wTG~rW~VslS~g~~~--------  135 (165)
                      ..++..-.=..|..+|--|--+.. ..+.+.+.+.+.-    ......+|...|.+.-|+.-.|.+..|...        
T Consensus       600 ~~lv~~L~l~glvrqLA~ns~~~~-~~~~l~L~L~~~q~hL~~~~~~~~L~~ALs~~lg~~i~l~Ie~g~~~eTP~~~~~  678 (717)
T PRK08853        600 SALITKLETPKLVEQLALNSAFVK-QGSQISLTLRSSQAHLNTDKAQEELLQALNEVLGEECHLSIEVGEEGETPLELRE  678 (717)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHC-CCCEEEEEECHHHHHHCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCHHHHHH
T ss_conf             999987687089999998426220-2998899877788875699999999999999868986899986998889999999


Q ss_pred             -----------HHHHCCHHHHHHHHHCCCCEE--EEEEEC
Q ss_conf             -----------366539699999986799778--987745
Q 537021.9.peg.4  136 -----------EYFEIDSDIKAVRTIFPTAQV--VCIRTI  162 (165)
Q Consensus       136 -----------e~~~~dp~V~avl~~FPgAeI--~~VR~~  162 (165)
                                 +.++.||.|+..++.| ||+|  -+||++
T Consensus       679 r~~~e~~~qA~~~L~~Dp~VQ~L~~~F-~A~l~~~SIrPl  717 (717)
T PRK08853        679 RLYQQKLQQALQSLENDPHVQFIERRF-AAELDQDSVRPI  717 (717)
T ss_pred             HHHHHHHHHHHHHHHCCHHHHHHHHHC-CCEECCCCEEEC
T ss_conf             999999999999996399999999973-988847851119


No 14 
>PRK08451 DNA polymerase III subunits gamma and tau; Validated
Probab=74.01  E-value=8  Score=19.80  Aligned_cols=96  Identities=13%  Similarity=0.200  Sum_probs=59.6

Q ss_pred             CCCHHHHHHHHHHCCHHHHHHHHHHCCCCEEECCCEEEEEEC-CCCCHHHHHHH----HHHHHHHCCCCEEEEEE-----
Q ss_conf             244899999998618266799997264004504980899977-89997799999----99999860992599996-----
Q 537021.9.peg.4   61 DNYTKQLIELCEKNHDYKMVEMLQRFLHVVSFELGRLEVSFL-KEIPEDFIENL----ATKLKNWTGEDWEIRFS-----  130 (165)
Q Consensus        61 ~nsf~~lveL~~~~rei~Lk~~Le~~VrLVsFe~GrIei~~~-~~a~~~l~~~L----s~~L~~wTG~rW~VslS-----  130 (165)
                      .+.|+.++.-..+. +..|..-.+.+++.|+|+.+.+.+.-. .+-.+.++..-    ..++.+--|.+-.|-.-     
T Consensus       375 ~~~~~~~~~ki~dr-~~elg~~f~~~~~f~~f~~~~l~~~s~a~~~~~~~l~~~~~~i~~~~~~~fg~~~~i~~~~~~~~  453 (523)
T PRK08451        375 KNLFEQLVAKIYDR-NYELGECFEKNIRFIDFDNNTLTWESNAQGEDKELLRKGFKIIKEIVKEVFGKGAKIKIAKKNHS  453 (523)
T ss_pred             CCHHHHHHHHHHHH-HHHHHHHHHHCEEEEECCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCH
T ss_conf             34599999987440-18899998715367763577678873467436898861169999999998414501235542120


Q ss_pred             ------------------------C-----------------CCCHHHHHCCHHHHHHHHHCCCCEEE
Q ss_conf             ------------------------8-----------------97413665396999999867997789
Q 537021.9.peg.4  131 ------------------------L-----------------GRCCEYFEIDSDIKAVRTIFPTAQVV  157 (165)
Q Consensus       131 ------------------------~-----------------g~~~e~~~~dp~V~avl~~FPgAeI~  157 (165)
                                              .                 ....+.+..+|.|+++.+.|-.-+|.
T Consensus       454 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ak~lfg~~~v~  521 (523)
T PRK08451        454 ENKSEPEPPKTVKENKISSLKKELPNNENKEIDEQSSIEMPKELQKFFINQEDLIEEAKDLFGEKSIE  521 (523)
T ss_pred             HHCCCCCCCCCCCHHCCHHHHHHHCCCCCCCCHHCCCCCCHHHHCCCCCCCCHHHHHHHHHHCCCHHC
T ss_conf             20135677543320014147776137754551010353464443002477706999999973821100


No 15 
>PTZ00105 60S ribosomal protein L12; Provisional
Probab=57.08  E-value=11  Score=18.98  Aligned_cols=52  Identities=13%  Similarity=0.182  Sum_probs=45.6

Q ss_pred             CHHHHHHHHHHCCHHHHHHHHHHCCCCEEECCCEEEEEECCCCCHHHHHHHH
Q ss_conf             4899999998618266799997264004504980899977899977999999
Q 537021.9.peg.4   63 YTKQLIELCEKNHDYKMVEMLQRFLHVVSFELGRLEVSFLKEIPEDFIENLA  114 (165)
Q Consensus        63 sf~~lveL~~~~rei~Lk~~Le~~VrLVsFe~GrIei~~~~~a~~~l~~~Ls  114 (165)
                      +|++++++++.+++-.+.++|..-|+-|-=-...+-+......|+++..++.
T Consensus       105 t~eqv~~IAk~k~~~l~a~~l~~avKeVlGTa~SmG~tVeGk~Pkev~~~I~  156 (164)
T PTZ00105        105 TFEQVIKIAKEMREKSMAKTFKGTVKEVLGTAQSIGCTVDGQSPRDIQEKID  156 (164)
T ss_pred             CHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCEEEEEEECCCCHHHHHHHHH
T ss_conf             8999999999977652462077779987600237268854989899999874


No 16 
>pfam10273 WGG Pre-rRNA-processing protein TSR2. This entry represents the central conserved section of a family of proteins described as pre-rRNA-processing protein TSR2. The region has a distinctive WGG motif but the function is unknown.
Probab=49.18  E-value=3  Score=22.27  Aligned_cols=50  Identities=18%  Similarity=0.148  Sum_probs=42.9

Q ss_pred             HHHHHHHHHHHHCCCCEEEEEECCCCHHHHHCCHHHHHHHHHCCCCEEEE
Q ss_conf             99999999998609925999968974136653969999998679977898
Q 537021.9.peg.4  109 FIENLATKLKNWTGEDWEIRFSLGRCCEYFEIDSDIKAVRTIFPTAQVVC  158 (165)
Q Consensus       109 l~~~Ls~~L~~wTG~rW~VslS~g~~~e~~~~dp~V~avl~~FPgAeI~~  158 (165)
                      |..-+...|..||..|-.|.-+-|++-...+++-++..|.+.|...+.++
T Consensus         2 F~~~V~~~l~~W~aL~lAVen~wGG~~S~~K~~~l~~~i~~~f~~~~~~~   51 (82)
T pfam10273         2 FELGVGLVLSRWTALQLAVENNWGGPDSAEKADWLAGAIVDLFTENKDVD   51 (82)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             88999999934699999999135896789999999999999986489999


No 17 
>pfam01610 Transposase_12 Transposase. Transposase proteins are necessary for efficient DNA transposition. Contains transposases for IS204, IS1001, IS1096, and IS1165.
Probab=48.57  E-value=24  Score=17.00  Aligned_cols=63  Identities=24%  Similarity=0.248  Sum_probs=34.8

Q ss_pred             CCEEECCCEEEEEECCCCCHHHHHHHHHHHHHHCCCC--EEEEEECCCCHHHHHCCHHHHHHHHHCCCCEEEEEE
Q ss_conf             0045049808999778999779999999999860992--599996897413665396999999867997789877
Q 537021.9.peg.4   88 HVVSFELGRLEVSFLKEIPEDFIENLATKLKNWTGED--WEIRFSLGRCCEYFEIDSDIKAVRTIFPTAQVVCIR  160 (165)
Q Consensus        88 rLVsFe~GrIei~~~~~a~~~l~~~Ls~~L~~wTG~r--W~VslS~g~~~e~~~~dp~V~avl~~FPgAeI~~VR  160 (165)
                      -++-++.|++- ...++-.   ...|..+|....+..  =+-.++.+      -..|..+++-+.||.|.|+-=|
T Consensus        18 vv~D~~~~~vl-~i~~gR~---~~~l~~~~~~~~~~~~~~V~~V~~D------m~~~y~~~v~~~~P~A~iv~Dr   82 (100)
T pfam01610        18 IIVDLETRKIL-DILPGRS---KETLKEYLRLRPERAREQVEVVSMD------MSSPYKDAVRELFPNAKIVADR   82 (100)
T ss_pred             EEEECCCCEEE-EEECCCC---HHHHHHHHHHCCHHHHCCEEEEECC------CCHHHHHHHHHHCCCCCEEEEH
T ss_conf             99968999899-9809998---7899999997897540316999835------7689999999978998298214


No 18 
>pfam05637 Glyco_transf_34 galactosyl transferase GMA12/MNN10 family. This family contains a number of glycosyltransferase enzymes that contain a DXD motif. This family includes a number of C. elegans homologues where the DXD is replaced by DXH. Some members of this family are included in glycosyltransferase family 34.
Probab=44.40  E-value=15  Score=18.14  Aligned_cols=18  Identities=17%  Similarity=0.206  Sum_probs=11.6

Q ss_pred             HCCHHHHHHHHHCCCCEE
Q ss_conf             539699999986799778
Q 537021.9.peg.4  139 EIDSDIKAVRTIFPTAQV  156 (165)
Q Consensus       139 ~~dp~V~avl~~FPgAeI  156 (165)
                      .+=|+|+++|.+||.||=
T Consensus        62 ~Kv~~iR~aM~~~P~aew   79 (242)
T pfam05637        62 AKLPAIRQTMKKYPDAEW   79 (242)
T ss_pred             EHHHHHHHHHHHCCCCEE
T ss_conf             268999999998899349


No 19 
>COG0193 Pth Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=39.49  E-value=32  Score=16.25  Aligned_cols=61  Identities=15%  Similarity=0.253  Sum_probs=41.3

Q ss_pred             EEECCCEEEEEECCCCC-HHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHCCHHHHHHHHHCCCCE
Q ss_conf             45049808999778999-7799999999998609925999968974136653969999998679977
Q 537021.9.peg.4   90 VSFELGRLEVSFLKEIP-EDFIENLATKLKNWTGEDWEIRFSLGRCCEYFEIDSDIKAVRTIFPTAQ  155 (165)
Q Consensus        90 VsFe~GrIei~~~~~a~-~~l~~~Ls~~L~~wTG~rW~VslS~g~~~e~~~~dp~V~avl~~FPgAe  155 (165)
                      +.+.+|++-++...++- .+=++++...|.  |..=|-+.+-=||+.   ..+..+.=||..|+.+|
T Consensus        95 Ldl~~G~vrlk~~Gg~gGHNGlKSi~~~lG--t~~f~RlRiGIGrP~---~~~~v~~~VL~~f~~~E  156 (190)
T COG0193          95 LDLPLGKVRLKLGGGAGGHNGLKSIIAHLG--TNNFYRLRIGIGRPG---NGEDVADYVLGKFSKEE  156 (190)
T ss_pred             CCCCCCEEEEECCCCCCCCCCHHHHHHHHC--CCCCCEEEEECCCCC---CCCCHHHHHCCCCCHHH
T ss_conf             678887389974889888455999999849--886206998758899---88836676358999899


No 20 
>KOG1559 consensus
Probab=38.87  E-value=25  Score=16.85  Aligned_cols=68  Identities=12%  Similarity=0.085  Sum_probs=56.8

Q ss_pred             CHHHHHHHHHHCCHHHHHHHHHHCCCCEEECC-CEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEE
Q ss_conf             48999999986182667999972640045049-808999778999779999999999860992599996
Q 537021.9.peg.4   63 YTKQLIELCEKNHDYKMVEMLQRFLHVVSFEL-GRLEVSFLKEIPEDFIENLATKLKNWTGEDWEIRFS  130 (165)
Q Consensus        63 sf~~lveL~~~~rei~Lk~~Le~~VrLVsFe~-GrIei~~~~~a~~~l~~~Ls~~L~~wTG~rW~VslS  130 (165)
                      -|+.|--++.++||++-+++-++..-...|-. |.|+=+.-.+-|.++...|+.--.-....+|-|+.-
T Consensus       156 GFE~lsmiISqnrdile~~d~vd~AssLqF~~nvn~~~t~FQrFPpELLkkL~~dcLvmq~Hk~gisp~  224 (340)
T KOG1559         156 GFELLSMIISQNRDILERFDAVDVASSLQFVGNVNIHGTMFQRFPPELLKKLSTDCLVMQNHKFGISPK  224 (340)
T ss_pred             HHHHHHHHHHCCHHHHHHHCCCCCCCCEEEECCCCEEEHHHHHCCHHHHHHHCCCHHEEECCCCCCCHH
T ss_conf             389999998557068775032021353023035540011575489999987352311000332344623


No 21 
>PRK06156 hypothetical protein; Provisional
Probab=38.16  E-value=35  Score=16.03  Aligned_cols=69  Identities=17%  Similarity=0.135  Sum_probs=48.2

Q ss_pred             HHHCCCCEEECCCEEEEEECCCCC-----HHHHHHHHHHHHHHCCCC-EEEEE--ECCCCHHHHHCCHHHHHHHHHC
Q ss_conf             972640045049808999778999-----779999999999860992-59999--6897413665396999999867
Q 537021.9.peg.4   83 LQRFLHVVSFELGRLEVSFLKEIP-----EDFIENLATKLKNWTGED-WEIRF--SLGRCCEYFEIDSDIKAVRTIF  151 (165)
Q Consensus        83 Le~~VrLVsFe~GrIei~~~~~a~-----~~l~~~Ls~~L~~wTG~r-W~Vsl--S~g~~~e~~~~dp~V~avl~~F  151 (165)
                      |--++-+++++.+++++.++=+-|     ..+..++...|..|.... ..+.+  +.+.+.-.-..+|+|+..|+++
T Consensus       375 LT~n~gii~~~~~~~~l~iniRyPv~~~~e~l~~~i~~~l~~~~~~~~~~l~i~~~~~~P~yv~~dsplVqtLl~vY  451 (522)
T PRK06156        375 LTLSPTVVKQTDKGTEVTVNLRRPVGKTPELLKGEIAEALAKWQAKHQVTLDIDTYWGEPMVRDPKGPWLQTLLDVF  451 (522)
T ss_pred             CEEEEEEEEEECCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCEEECCCCHHHHHHHHHH
T ss_conf             47986899997988999999968898888999999999999878752836987522688644598998999999999


No 22 
>pfam10411 DsbC_N Disulfide bond isomerase protein N-terminus. This is the N-terminal domain of the disulfide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerization. DsbC is required for disulfide bond formation and functions as a disulfide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity.
Probab=36.72  E-value=27  Score=16.65  Aligned_cols=19  Identities=21%  Similarity=0.586  Sum_probs=16.2

Q ss_pred             HHHHHHCCCCEEEEEEECC
Q ss_conf             9999867997789877458
Q 537021.9.peg.4  145 KAVRTIFPTAQVVCIRTIP  163 (165)
Q Consensus       145 ~avl~~FPgAeI~~VR~~p  163 (165)
                      +++..+||+++|.+|..-|
T Consensus         3 ~~l~~~~p~~~v~~v~~sp   21 (54)
T pfam10411         3 QALKKLLPGLKVESVKPSP   21 (54)
T ss_pred             HHHHHHCCCCCEEEEECCC
T ss_conf             6988768899613887578


No 23 
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=32.78  E-value=33  Score=16.22  Aligned_cols=16  Identities=38%  Similarity=0.559  Sum_probs=12.6

Q ss_pred             HHHHHHHHHCCCCEEE
Q ss_conf             6999999867997789
Q 537021.9.peg.4  142 SDIKAVRTIFPTAQVV  157 (165)
Q Consensus       142 p~V~avl~~FPgAeI~  157 (165)
                      ..|++.+.+|||+||-
T Consensus        20 ~~V~~~i~alpg~EIh   35 (87)
T PRK10553         20 SDISTQLNAFPGCEVA   35 (87)
T ss_pred             HHHHHHHHHCCCCEEE
T ss_conf             9999999708997871


No 24 
>TIGR01734 D-ala-DACP-lig D-alanine-activating enzyme; InterPro: IPR010072   This entry represents the enzyme (also called D-alanine-D-alanyl carrier protein ligase) which activates D-alanine as an adenylate via the reaction D-ala + ATP to D-ala-AMP + PPi, and further catalyses the condensation of the amino acid adenylate with the D-alanyl carrier protein (D-ala-ACP). The D-alanine is then further transferred to teichoic acid in the biosynthesis of lipoteichoic acid (LTA) and wall teichoic acid (WTA) in Gram-positive bacteria, both polysacchatides .; GO: 0016208 AMP binding, 0047473 D-alanine-poly(phosphoribitol) ligase activity, 0019350 teichoic acid biosynthetic process.
Probab=32.68  E-value=26  Score=16.78  Aligned_cols=19  Identities=26%  Similarity=0.363  Sum_probs=15.0

Q ss_pred             CCHHHHHHHHHCCCCEEEE
Q ss_conf             3969999998679977898
Q 537021.9.peg.4  140 IDSDIKAVRTIFPTAQVVC  158 (165)
Q Consensus       140 ~dp~V~avl~~FPgAeI~~  158 (165)
                      ....=+|.+++||.|.|-.
T Consensus       278 ~~ktA~~Ll~RFP~A~IyN  296 (513)
T TIGR01734       278 TKKTAKALLERFPSATIYN  296 (513)
T ss_pred             HHHHHHHHHHHCCCCEEEC
T ss_conf             2689999984188977974


No 25 
>pfam04461 DUF520 Protein of unknown function (DUF520). Family of uncharacterized proteins.
Probab=30.92  E-value=46  Score=15.33  Aligned_cols=82  Identities=13%  Similarity=0.229  Sum_probs=54.3

Q ss_pred             HHCCHHHHHHHHHHCCCCEEECCCEEE----------EEECCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHCC
Q ss_conf             861826679999726400450498089----------9977899977999999999986099259999689741366539
Q 537021.9.peg.4   72 EKNHDYKMVEMLQRFLHVVSFELGRLE----------VSFLKEIPEDFIENLATKLKNWTGEDWEIRFSLGRCCEYFEID  141 (165)
Q Consensus        72 ~~~rei~Lk~~Le~~VrLVsFe~GrIe----------i~~~~~a~~~l~~~Ls~~L~~wTG~rW~VslS~g~~~e~~~~d  141 (165)
                      ..-.|++....++++|-+-.|+.|.+|          +.+..+.+.+.++.+.+.+.+-- ..-+.++-++.-.-+-+.-
T Consensus        57 ~~~~diL~~k~~KR~i~~k~ld~~~~e~asG~~~rq~i~lk~GI~~e~AKkI~K~IK~~k-lKVqa~IQGd~vRVsgKkr  135 (160)
T pfam04461        57 KQVKDILRTKLIKRGVDLKALDFGKVEKASGKTVKQEVKLKQGIDQELAKKIVKLIKDSK-LKVQAAIQGDQVRVTGKKR  135 (160)
T ss_pred             HHHHHHHHHHHHHCCCCCCEECCCCCCCCCCCEEEEEEEHHCCCCHHHHHHHHHHHHHCC-CCEEEEECCCEEEEECCCH
T ss_conf             999999999998539981101358742467987999988220438899999999998448-8036886485788615988


Q ss_pred             HHHHHHHHHCCCC
Q ss_conf             6999999867997
Q 537021.9.peg.4  142 SDIKAVRTIFPTA  154 (165)
Q Consensus       142 p~V~avl~~FPgA  154 (165)
                      ...|+|++..-++
T Consensus       136 DDLQ~vi~~lK~~  148 (160)
T pfam04461       136 DDLQAVIALLREA  148 (160)
T ss_pred             HHHHHHHHHHHHC
T ss_conf             8999999999832


No 26 
>KOG2492 consensus
Probab=29.17  E-value=49  Score=15.15  Aligned_cols=69  Identities=14%  Similarity=0.184  Sum_probs=55.6

Q ss_pred             CEEECCCEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEECC-----------CCHHHHHCCHHHHHHHHHCCCCEEE
Q ss_conf             04504980899977899977999999999986099259999689-----------7413665396999999867997789
Q 537021.9.peg.4   89 VVSFELGRLEVSFLKEIPEDFIENLATKLKNWTGEDWEIRFSLG-----------RCCEYFEIDSDIKAVRTIFPTAQVV  157 (165)
Q Consensus        89 LVsFe~GrIei~~~~~a~~~l~~~Ls~~L~~wTG~rW~VslS~g-----------~~~e~~~~dp~V~avl~~FPgAeI~  157 (165)
                      -|+-+...+-|+|++--|+||+-++-..+.+--..-=++.+-.+           |+-...++-|+|+.|-+..||.-+.
T Consensus       318 ~vs~~~PemR~RFTSPHPKDfpdevl~li~~rdnickqihlPAqSgds~vLE~mrRgysreayl~lv~~Irs~iPgVgls  397 (552)
T KOG2492         318 QVSRADPEMRIRFTSPHPKDFPDEVLELIRDRDNICKQIHLPAQSGDSRVLEIMRRGYSREAYLELVAHIRSMIPGVGLS  397 (552)
T ss_pred             HHHHHCCCEEEEECCCCCCCCHHHHHHHHHHCCCHHHEEECCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCE
T ss_conf             88652865078736999877739999998817531422425666885489999870578676534777788658887632


No 27 
>pfam11396 DUF2874 Protein of unknown function (DUF2874). This bacterial family of proteins are probable periplasmic proteins with unknown function. There are between one and four copies of this domain per sequence.
Probab=28.46  E-value=51  Score=15.08  Aligned_cols=22  Identities=18%  Similarity=0.347  Sum_probs=17.5

Q ss_pred             HHHHHHHHHCCCCEEEEEEECC
Q ss_conf             6999999867997789877458
Q 537021.9.peg.4  142 SDIKAVRTIFPTAQVVCIRTIP  163 (165)
Q Consensus       142 p~V~avl~~FPgAeI~~VR~~p  163 (165)
                      +...++.+.||||.|.++....
T Consensus         4 ~V~~~i~~~y~~~~i~~~e~~~   25 (54)
T pfam11396         4 AVKNAIKKSYPGAKIVEVEKEE   25 (54)
T ss_pred             HHHHHHHHHCCCCEEEEEEEEE
T ss_conf             9999999878997788999998


No 28 
>TIGR01091 upp uracil phosphoribosyltransferase; InterPro: IPR005765    The enzyme uracil phosphoribosyltransferase (UPRT, 2.4.2.9 from EC) catalyzes conversion of uracil to uridine 5'-monophosphate utilizing 5'-phosphoribosyl--1-pyrophosphate (PRPP).  UMP + diphosphate = uracil + 5-phospho-alpha-D-ribose 1-diphosphate  ; GO: 0004845 uracil phosphoribosyltransferase activity, 0006223 uracil salvage.
Probab=24.40  E-value=61  Score=14.64  Aligned_cols=20  Identities=20%  Similarity=0.192  Sum_probs=16.7

Q ss_pred             CCHHHHHHHHHCCCCEEEEE
Q ss_conf             39699999986799778987
Q 537021.9.peg.4  140 IDSDIKAVRTIFPTAQVVCI  159 (165)
Q Consensus       140 ~dp~V~avl~~FPgAeI~~V  159 (165)
                      .=|+|=.|++.||.|+|.-|
T Consensus        83 GLgm~dG~~~~~P~A~vG~~  102 (213)
T TIGR01091        83 GLGMVDGVLKLIPEAKVGHV  102 (213)
T ss_pred             HHHHHHHHHHHCCCCEEEEE
T ss_conf             26899999984887718999


No 29 
>PRK05758 F0F1 ATP synthase subunit delta; Validated
Probab=23.58  E-value=63  Score=14.54  Aligned_cols=85  Identities=13%  Similarity=0.164  Sum_probs=59.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHCCCCEEECCCEEEEEEC--CCCCHHHHHHHHHHHHHHC
Q ss_conf             54443233210013471244899999998618266799997264004504980899977--8999779999999999860
Q 537021.9.peg.4   44 GITEKQDVLNRLSACTPDNYTKQLIELCEKNHDYKMVEMLQRFLHVVSFELGRLEVSFL--KEIPEDFIENLATKLKNWT  121 (165)
Q Consensus        44 ~~~~~~~~~~~~~~~~~~nsf~~lveL~~~~rei~Lk~~Le~~VrLVsFe~GrIei~~~--~~a~~~l~~~Ls~~L~~wT  121 (165)
                      +...+...............|  |--|++.+|-..|..-++.+..++.-..|......+  ..++.+...+|...|...+
T Consensus        54 ~~~~K~~il~~l~~~~~~~nf--l~lL~~~~R~~~l~~I~~~f~~l~~~~~~~~~~~V~sA~~Ls~~q~~~i~~~l~~~~  131 (175)
T PRK05758         54 SAEQKAELLIAVLDEAGQGNF--LKLLAENGRLALLPEIAEQFEALLAEHENIVDAEVTSAFPLSEEQLDKLKAALEKRL  131 (175)
T ss_pred             CHHHHHHHHHHHHCCCCHHHH--HHHHHHCCCHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCHHHHHHHHHHHHHHH
T ss_conf             999999999999745229999--999998884667999999999999985697999999788999999999999999996


Q ss_pred             CCCEEEEEE
Q ss_conf             992599996
Q 537021.9.peg.4  122 GEDWEIRFS  130 (165)
Q Consensus       122 G~rW~VslS  130 (165)
                      |..=.+...
T Consensus       132 gk~v~l~~~  140 (175)
T PRK05758        132 GRKVKLNVK  140 (175)
T ss_pred             CCCCCCEEE
T ss_conf             997310444


No 30 
>pfam03927 NapD NapD protein. Uncharacterized protein involved in formation of periplasmic nitrate reductase.
Probab=22.20  E-value=63  Score=14.54  Aligned_cols=17  Identities=24%  Similarity=0.438  Sum_probs=9.7

Q ss_pred             HHHHHHHHHCCCCEEEE
Q ss_conf             69999998679977898
Q 537021.9.peg.4  142 SDIKAVRTIFPTAQVVC  158 (165)
Q Consensus       142 p~V~avl~~FPgAeI~~  158 (165)
                      +.|++.+.++||+||-.
T Consensus        17 ~~V~~~l~~~pg~Eih~   33 (78)
T pfam03927        17 AEVKAAILALPGAEIHA   33 (78)
T ss_pred             HHHHHHHHCCCCCEEEC
T ss_conf             99999997499968863


No 31 
>PRK05412 nucleotide-binding protein; Reviewed
Probab=21.56  E-value=69  Score=14.30  Aligned_cols=81  Identities=14%  Similarity=0.200  Sum_probs=51.8

Q ss_pred             HCCHHHHHHHHHHCCCCEEECCCE----------EEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHCCH
Q ss_conf             618266799997264004504980----------8999778999779999999999860992599996897413665396
Q 537021.9.peg.4   73 KNHDYKMVEMLQRFLHVVSFELGR----------LEVSFLKEIPEDFIENLATKLKNWTGEDWEIRFSLGRCCEYFEIDS  142 (165)
Q Consensus        73 ~~rei~Lk~~Le~~VrLVsFe~Gr----------Iei~~~~~a~~~l~~~Ls~~L~~wTG~rW~VslS~g~~~e~~~~dp  142 (165)
                      .-.|++......|+|-+-.|+.|.          ..+.+..+.+.+.++.+.+.+.+-- ..-+.++-++.-.-+-+.-.
T Consensus        58 qv~diL~~kl~KR~i~~k~ld~~~~e~asG~~vrq~i~lk~GI~~e~AKkI~k~IK~~k-lKVqa~IQGd~vRVtgKkrD  136 (161)
T PRK05412         58 QVLDILRSKLIKRGIDLKALDYGKVEKASGKTVKQEVKLKQGIEQELAKKIVKLIKDSK-LKVQAQIQGDQVRVTGKKRD  136 (161)
T ss_pred             HHHHHHHHHHHHCCCCCCEECCCCCCCCCCCEEEEEEEHHCCCCHHHHHHHHHHHHHCC-CCEEEEECCCEEEEECCCHH
T ss_conf             99999999998539981101468843467987999988120438899999999998448-81368864857886159888


Q ss_pred             HHHHHHHHCCCC
Q ss_conf             999999867997
Q 537021.9.peg.4  143 DIKAVRTIFPTA  154 (165)
Q Consensus       143 ~V~avl~~FPgA  154 (165)
                      ..|+|+...-+.
T Consensus       137 DLQ~vi~llk~~  148 (161)
T PRK05412        137 DLQAVIALLRGA  148 (161)
T ss_pred             HHHHHHHHHHHC
T ss_conf             999999999832


No 32 
>TIGR02258 2_5_ligase 2'-5' RNA ligase; InterPro: IPR004175 Members of this entry are bacterial and archaeal RNA ligases that are able to ligate tRNA half molecules containing 2',3'-cyclic phosphate and 5' hydroxyl termini to products containing the 2',5' phosphodiester linkage. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family. The structure of a related protein is known . They belong to the 2H phosphoeseterase superfamily . They share a common active site, characterised by two conserved histidines, with vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins.; GO: 0008664 2'-5'-RNA ligase activity, 0016070 RNA metabolic process.
Probab=21.43  E-value=69  Score=14.28  Aligned_cols=61  Identities=21%  Similarity=0.237  Sum_probs=50.9

Q ss_pred             HHHHHHHHHCCHHHHHHHHHHCCCCEEECCCEEEEEECCCCCHHHHHHHHHHHHHHCCCC--EEEEEEC
Q ss_conf             999999986182667999972640045049808999778999779999999999860992--5999968
Q 537021.9.peg.4   65 KQLIELCEKNHDYKMVEMLQRFLHVVSFELGRLEVSFLKEIPEDFIENLATKLKNWTGED--WEIRFSL  131 (165)
Q Consensus        65 ~~lveL~~~~rei~Lk~~Le~~VrLVsFe~GrIei~~~~~a~~~l~~~Ls~~L~~wTG~r--W~VslS~  131 (165)
                      ++|.+++.+-+.      .-.++|.|.=|.=+|.+.|-..++.+.+.+|...|...+-..  -.+.|.+
T Consensus        15 ~~l~~~~~~~~~------~~~~~kwv~~en~HiTL~FLGe~~~~~~~~l~~~L~~~~~~~~~F~l~l~g   77 (189)
T TIGR02258        15 EQLSEIQRKLKS------ELSGIKWVPPENLHITLKFLGEVDEEQVEELEDALAKIAEPPEPFTLKLEG   77 (189)
T ss_pred             HHHHHHHHHHHC------CCCCCEEECCCCCEEEEEEECCCCHHHHHHHHHHHHHHHCCCCCCEEEEEE
T ss_conf             999999998510------256761206666313122435799889999999888750389973478752


No 33 
>PRK13552 frdB fumarate reductase iron-sulfur subunit; Provisional
Probab=21.31  E-value=66  Score=14.40  Aligned_cols=45  Identities=13%  Similarity=0.102  Sum_probs=36.2

Q ss_pred             CCCEEECCCEEEEEECCCCC--HHHHHHHHHHHHHHC--CCCEEEEEEC
Q ss_conf             40045049808999778999--779999999999860--9925999968
Q 537021.9.peg.4   87 LHVVSFELGRLEVSFLKEIP--EDFIENLATKLKNWT--GEDWEIRFSL  131 (165)
Q Consensus        87 VrLVsFe~GrIei~~~~~a~--~~l~~~Ls~~L~~wT--G~rW~VslS~  131 (165)
                      .++-+|+.|.|++.+..+.|  +||+-+.+.|...+.  ...|+..-+.
T Consensus        79 t~v~~~~~~~i~iePl~~fpVIkDLVVD~~~f~~~~~~~v~~~l~~~~~  127 (240)
T PRK13552         79 TLTSDYPDGVITLMPLPVFKLIGDLSVNTGKWFREMAERVESWLHTKKE  127 (240)
T ss_pred             CCHHHCCCCCEEEEECCCCCCCCCCEEECHHHHHHHHHHCCCEECCCCC
T ss_conf             4000068995799889999611356540489999998616515426988


No 34 
>cd01791 Ubl5 UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved.  At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers.  ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=20.10  E-value=74  Score=14.12  Aligned_cols=23  Identities=30%  Similarity=0.315  Sum_probs=20.3

Q ss_pred             CCHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             99779999999999860992599
Q 537021.9.peg.4  105 IPEDFIENLATKLKNWTGEDWEI  127 (165)
Q Consensus       105 a~~~l~~~Ls~~L~~wTG~rW~V  127 (165)
                      .|.|-+++|.+.+..-||.||-=
T Consensus        19 ~~~DtIgdlKkliAaq~Gt~~~k   41 (73)
T cd01791          19 NPDDTIGDLKKLIAAQTGTRPEK   41 (73)
T ss_pred             CCCCCHHHHHHHHHHHHCCCHHH
T ss_conf             89873778999999985898333


Done!